Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
Trimmomatic was developed at the Usadel lab in Aachen, Germany.

The current trimming steps are:

ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.

SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold.

LEADING: Cut bases off the start of a read, if below a threshold quality

TRAILING: Cut bases off the end of a read, if below a threshold quality

CROP: Cut the read to a specified length

HEADCROP: Cut the specified number of bases from the start of the read

MINLEN: Drop the read if it is below a specified length

TOPHRED33: Convert quality scores to Phred-33

TOPHRED64: Convert quality scores to Phred-64

It works with FASTQ (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used), either uncompressed or gzipp'ed FASTQ. Use of gzip format is determined based on the .gz extension.

For single-ended data, one input and one output file are specified, plus the processing steps. For paired-end data, two input files are specified, and 4 output files, 2 for the 'paired' output where both reads survived the processing, and 2 for corresponding 'unpaired' output where a read survived, but the partner read did not.

Use the modules commands to set up trimmomatic, as in the example below. By loading the module, you will set up an alias called 'trimmomatic' which is equivalent to 'java -classpath /usr/local/apps/trimmomatic/Trimmomatic-0.25/trimmomatic-0.25.jar'. The module will also set an environment variable called 'TRIMMOJAR' which points to the location of the trimmomatic java file.

The first sample trimmomatic command in this example uses the 'trimmomatic' alias. The second sample command requests 2g of memory (larger than the default 1g set by the trimmatic alias), and uses the $TRIMMOJAR environment variable.